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I am trying to install (update) my local version of GalSim software on Ubuntu 14.04 by running SCons. I have all the dependencies (boost, TMV etc.) installed and have used it for quite a while now. I use Python2.7. But now, when I run scons from the terminal, I get the following error:

scons: Reading SConscript files ...
SCons is version 2.3.0 using python version 2.7.6
Python is from /usr/include/python
Using the following (non-default) scons options:
PYPREFIX = /usr/lib/python2.7/dist-packages/
TMV_DIR = /media/arunkannawadi/Acads_CMU/Cosmology/WFIRST_Project/tmv0.72/
These can be edited directly in the file gs_scons.conf.
Type scons -h for a full list of available options.
Using python =  /usr/bin/python
Using compiler: /usr/bin/g++
compiler version: 4.8.2
Determined that a good number of jobs = 4
Checking for C++ header file fftw3.h... yes
Checking for correct FFTW linkage... yes
Checking for boost header files... yes
Boost version is 1.54.0
Checking for C++ header file TMV.h... yes
TMV version is 0.72
Using TMV_LINK file: /media/arunkannawadi/Acads_CMU/Cosmology   /WFIRST_Project/tmv0.72/share/tmv-link
-ltmv -lblas -lgfortran -lpthread -fopenmp
Checking for correct TMV linkage... (this may take a little while)
Checking for correct TMV linkage... yes
Checking if we can build against Python...
Unable to get python include path python executable: 
/usr/bin/python

Please fix the above error(s) and rerun scons.
Note: you may want to look through the file INSTALL.md for advice.
Also, if you are having trouble, please check the INSTALL FAQ at
https://github.com/GalSim-developers/GalSim/wiki/Installation%20FAQ

The output of which python is /usr/bin/python and the output of python --version is Python 2.7.6.

Arun Kannawadi
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1 Answers1

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Upon further investigation, this question is not about GalSim per se, but rather points out an oddity of later Ubuntu versions.

After going over the config.log file from the failed installation (not posted here), it became apparent that the tests of the installation were passing, but there was a failure in parsing the outputs of those tests. The error message was

sh: 1: Syntax error: Bad fd number

A search pointed me to this other question about that error message: sh: Syntax error: Bad fd number which points out that that in Ubuntu 11.x /bin/sh is linked to /bin/dash and not to bin bash. So, the fix for this apparent problem with GalSim installation is to use the solution on that page to correctly link /bin/sh to bash.

Community
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rmandelb
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  • Apparently the problem is really that we are using `>&` to redirect stderr to stdout. While this is widespread common practice, it is apparently not posix-compliant. Just something that bash allows to be more accommodating to people coming from csh, where that is the proper syntax. cf. http://ubuntuforums.org/showthread.php?t=1460684 and http://unix.stackexchange.com/questions/118303/why-does-nohup-command-dev-null-seem-to-work-in-some-shells The posix-compliant thing that works for both dash and bash is apparently `cmd > file 2>&1` – Mike Jarvis Jul 22 '15 at 14:10
  • Thanks! This fixed the problem! – Arun Kannawadi Jul 22 '15 at 16:27
  • Update: I fixed this on master, so the next release of GalSim shouldn't have this problem with non-bash shells. Specifically, I reproduced your failure when /bin/sh is really dash, and the update fixed the problem. – Mike Jarvis Sep 15 '15 at 17:32